                      :-) GROMACS - gmx mdrun, 2022.3 (-:

Copyright 1991-2022 The GROMACS Authors.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

                         Current GROMACS contributors:
       Mark Abraham           Andrey Alekseenko           Cathrine Bergh      
      Christian Blau            Eliane Briand               Kevin Boyd        
     Oliver Fleetwood         Stefan Fleischmann           Vytas Gapsys       
       Gaurav Garg           Gilles Gouaillardet            Alan Gray         
      Victor Holanda           M. Eric Irrgang              Joe Jordan        
    Christoph Junghans        Prashanth Kanduri           Sebastian Kehl      
     Sebastian Keller          Carsten Kutzner           Magnus Lundborg      
       Pascal Merz              Dmitry Morozov             Szilard Pall       
      Roland Schulz             Michael Shirts         David van der Spoel    
     Alessandra Villa      Sebastian Wingbermuehle        Artem Zhmurov       

                         Previous GROMACS contributors:
        Emile Apol             Rossen Apostolov           James Barnett       
  Herman J.C. Berendsen          Par Bjelkmar           Viacheslav Bolnykh    
    Aldert van Buuren          Carlo Camilloni           Rudi van Drunen      
      Anton Feenstra           Gerrit Groenhof            Bert de Groot       
      Anca Hamuraru           Vincent Hindriksen         Aleksei Iupinov      
   Dimitrios Karkoulis           Peter Kasson               Jiri Kraus        
       Per Larsson             Justin A. Lemkul           Viveca Lindahl      
      Erik Marklund           Pieter Meulenhoff           Vedran Miletic      
      Teemu Murtola              Sander Pronk            Alexey Shvetsov      
      Alfons Sijbers            Peter Tieleman             Jon Vincent        
     Teemu Virolainen         Christian Wennberg           Maarten Wolf       

                  Coordinated by the GROMACS project leaders:
                    Paul Bauer, Berk Hess, and Erik Lindahl

GROMACS:      gmx mdrun, version 2022.3
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/bioinfo/My Passport/2xwt-rs1-311k-400ns
Process ID:   407419
Command line:
  gmx mdrun -deffnm md_0_10 -v

GROMACS version:    2022.3
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        CUDA
SIMD instructions:  NONE
CPU FFT library:    fftw-3.3.8
GPU FFT library:    cuFFT
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 11.4.0
C compiler flags:   -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Wed_Sep_21_10:33:58_PDT_2022;Cuda compilation tools, release 11.8, V11.8.89;Build cuda_11.8.r11.8/compiler.31833905_0
CUDA compiler flags:-std=c++17;;-D_FORCE_INLINES;-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA driver:        12.20
CUDA runtime:       11.80


Running on 1 node with total 6 cores, 12 processing units, 1 compatible GPU
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) W-2133 CPU @ 3.60GHz
    Family: 6   Model: 85   Stepping: 4
    Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
    Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2
  Hardware topology: Basic
    Packages, cores, and logical processors:
    [indices refer to OS logical processors]
      Package  0: [   0   6] [   1   7] [   2   8] [   3   9] [   4  10] [   5  11]
    CPU limit set by OS: -1   Recommended max number of threads: 12
  GPU info:
    Number of GPUs detected: 1
    #0: NVIDIA Quadro P4000, compute cap.: 6.1, ECC:  no, stat: compatible

Highest SIMD level supported by all nodes in run: AVX_512
SIMD instructions selected at compile time:       None
This program was compiled for different hardware than you are running on,
which could influence performance.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.7037338
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 200000000
   init-step                      = 0
   simulation-part                = 1
   mts                            = false
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = -1744830593
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 80
   fourier-ny                     = 80
   fourier-nz                     = 80
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 3d
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
     density-guided-simulation:
       active                     = false
       group                      = protein
       similarity-measure         = inner-product
       atom-spreading-weight      = unity
       force-constant             = 1e+09
       gaussian-transform-spreading-width = 0.2
       gaussian-transform-spreading-range-in-multiples-of-width = 4
       reference-density-filename = reference.mrc
       nst                        = 1
       normalize-densities        = true
       adaptive-force-scaling     = false
       adaptive-force-scaling-time-constant = 4
       shift-vector               = 
       transformation-matrix      = 
     qmmm-cp2k:
       active                     = false
       qmgroup                    = System
       qmmethod                   = PBE
       qmfilenames                = 
       qmcharge                   = 0
       qmmultiplicity             = 1
grpopts:
   nrdf:     25662.7      245994
   ref-t:         311         311
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0

Changing nstlist from 10 to 100, rlist from 1 to 1.163

When checking whether update groups are usable:
  Domain decomposition is not active, so there is no need for update groups
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 12 OpenMP threads 

Pinning threads with an auto-selected logical cpu stride of 1
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Coulomb Ewald tables, spacing: 9.33e-04 size: 1073

Generated table with 1081 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1081 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1081 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: <C6> 3.2562e-04


Using GPU 8x8 nonbonded short-range kernels

Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning:
  outer list: updated every 100 steps, buffer 0.163 nm, rlist 1.163 nm
  inner list: updated every  12 steps, buffer 0.006 nm, rlist 1.006 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 100 steps, buffer 0.317 nm, rlist 1.317 nm
  inner list: updated every  12 steps, buffer 0.055 nm, rlist 1.055 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 5102

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 133250 Atoms
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

Started mdrun on rank 0 Fri Jun  7 10:09:10 2024

           Step           Time
              0        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    8.15284e+03    2.34378e+04    1.64732e+04    1.34556e+03   -3.95822e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    7.37308e+03    1.47111e+05    2.72125e+05   -1.78450e+04   -2.18675e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.24182e+04   -1.72012e+06    3.51597e+05   -1.36852e+06   -1.36844e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11329e+02   -2.18882e+02    1.99582e+02    4.43027e-06

step 1000: timed with pme grid 80 80 80, coulomb cutoff 1.000: 1775.5 M-cycles
step 1200: timed with pme grid 64 64 64, coulomb cutoff 1.213: 2371.4 M-cycles
step 1400: timed with pme grid 72 72 72, coulomb cutoff 1.078: 1925.6 M-cycles
step 1600: timed with pme grid 80 80 80, coulomb cutoff 1.000: 1793.1 M-cycles
              optimal pme grid 80 80 80, coulomb cutoff 1.000


Received the INT signal, stopping within 100 steps

           Step           Time
           4700        9.40000

Writing checkpoint, step 4700 at Fri Jun  7 10:09:36 2024


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    8.59583e+03    2.41642e+04    1.66455e+04    1.45523e+03   -4.04513e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    7.34408e+03    1.46001e+05    2.69955e+05   -1.78162e+04   -2.18265e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.23064e+04   -1.71805e+06    3.50744e+05   -1.36730e+06   -1.36821e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.10574e+02   -2.18177e+02   -5.64882e+01    4.14939e-06


Energy conservation over simulation part #1 of length 9.4 ps, time 0 to 9.4 ps
  Conserved energy drift: 1.85e-04 kJ/mol/ps per atom


	<======  ###############  ==>
	<====  A V E R A G E S  ====>
	<==  ###############  ======>

	Statistics over 4701 steps using 48 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    8.44676e+03    2.38734e+04    1.67062e+04    1.39549e+03   -4.07456e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    7.20146e+03    1.46110e+05    2.72635e+05   -1.78217e+04   -2.18648e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.20485e+04   -1.71996e+06    3.51277e+05   -1.36869e+06   -1.36831e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11046e+02   -2.18311e+02   -2.14914e+00    0.00000e+00

          Box-X          Box-Y          Box-Z
    1.24276e+01    1.24276e+01    8.78767e+00

   Total Virial (kJ/mol)
    1.17853e+05   -2.66032e+02    3.72445e+02
   -2.67824e+02    1.17083e+05    2.64449e+02
    3.71116e+02    2.63982e+02    1.16611e+05

   Pressure (bar)
   -1.77559e+01    6.38726e+00   -1.06359e+01
    6.43112e+00   -3.73446e+00   -7.42344e+00
   -1.06034e+01   -7.41203e+00    1.50429e+01

      T-Protein  T-non-Protein
    3.11369e+02    3.11012e+02


	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check             571.326474        5141.938     0.0
 NxN Ewald Elec. + LJ [F]            610058.585664    40263866.654    98.0
 NxN Ewald Elec. + LJ [V&F]            6290.270464      673058.940     1.6
 1,4 nonbonded interactions             127.980024       11518.202     0.0
 Shift-X                                  6.396000          38.376     0.0
 Bonds                                   24.849486        1466.120     0.0
 Propers                                110.125626       25218.768     0.1
 Impropers                                7.770753        1616.317     0.0
 Virial                                  62.781945        1130.075     0.0
 Stop-CM                                  6.396000          63.960     0.0
 Calc-Ekin                              125.521500        3389.080     0.0
 Lincs                                   23.984502        1439.070     0.0
 Lincs-Mat                              124.839756         499.359     0.0
 Constraint-V                           626.135592        5635.220     0.0
 Constraint-Vir                          60.330390        1447.929     0.0
 Settle                                 192.722196       71307.213     0.2
 CMAP                                     3.140268        5338.456     0.0
 Urey-Bradley                            88.458717       16187.945     0.0
-----------------------------------------------------------------------------
 Total                                                41088363.622   100.0
-----------------------------------------------------------------------------


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 12 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Neighbor search        1   12         48       0.714         30.866   2.8
 Launch GPU ops.        1   12       4701       1.364         58.908   5.3
 Force                  1   12       4701       4.206        181.719  16.2
 Wait PME GPU gather    1   12       4701       1.924         83.097   7.4
 Reduce GPU PME F       1   12       4701       0.538         23.260   2.1
 Wait GPU NB local                              1.841         79.514   7.1
 NB X/F buffer ops.     1   12       9354       2.471        106.753   9.5
 Write traj.            1   12          2       0.376         16.236   1.4
 Update                 1   12       4701       1.059         45.741   4.1
 Constraints            1   12       4701       3.696        159.669  14.3
 Rest                                           7.745        334.607  29.9
-----------------------------------------------------------------------------
 Total                                         25.934       1120.371 100.0
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:      311.211       25.934     1200.0
                 (ns/day)    (hour/ns)
Performance:       31.323        0.766
Finished mdrun on rank 0 Fri Jun  7 10:09:36 2024

